gl.keep.loc: Removes all but the specified loci from a genlight object

In green-striped-gecko/dartR: Importing and Analysing 'SNP' and 'Silicodart' Data Generated by Genome-Wide Restriction Fragment Analysis

Removes all but the specified loci from a genlight object

Description

The script returns a genlight object with the all but the specified loci deleted.

#' See more about data manipulation in the [tutorial](http://georges.biomatix.org/storage/app/media/uploaded-files/tutorial4dartrdatamanipulation22-dec-21-3.pdf).

Usage

gl.keep.loc(x, loc.list = NULL, first = NULL, last = NULL, verbose = NULL)

Arguments

x	Name of the genlight object containing SNP genotypes or presence/absence data [required].
loc.list	A list of loci to be kept [required, if loc.range not specified].
first	First of a range of loci to be kept [required, if loc.list not specified].
last	Last of a range of loci to be kept [if not specified, last locus in the dataset].
verbose	Verbosity: 0, silent or fatal errors; 1, begin and end; 2, progress log; 3, progress and results summary; 5, full report [default 2 or as specified using gl.set.verbosity]

Value

A genlight object with the reduced data

Author(s)

Custodian: Arthur Georges – Post to https://groups.google.com/d/forum/dartr

See Also

gl.drop.loc to drop rather than keep specified loci

Examples

# SNP data
  gl2 <- gl.keep.loc(testset.gl, loc.list=c('100051468|42-A/T', '100049816-51-A/G'))
# Tag P/A data
  gs2 <- gl.keep.loc(testset.gs, loc.list=c('20134188','19249144'))

green-striped-gecko/dartR documentation built on Sept. 7, 2024, 4:15 a.m.